The study of the metabolism of oxygen by cytochrome oxidase (aa3), a binuclear iron copper redox center as compared with the mononuclear cytochrome Omicron types of oxidases sheds light on the essential sequence reactions in oxygen reduction. In cytochrome (aa3) oxidase the formation of bound peroxides, the rupture of the peroxide bond and the generation of radical intermediates form steps where sequestered and nonsequestered radical intermediates can render the system biologically safe or dangerous, respectively. The optical study of the steps in these radical reactions are complemented by studies of the charge densities of the metal atoms, the nature of the ligand shells and the distance to the nearest and next to nearest ligands in the radical intermediates by the use of X-ray synchrotron radiation to determine the edge and EXAFS (Extended X-Ray Absorption Fine Structure) properties. These studies form the basis for the understanding of normoxic and hyperoxic metabolism of oxygen and are essential to molecular explanations of processes leading to the pathway of fibrotic and interstitial lung disease.